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Molecular dynamics simulations of oligonucleotides in solution: Visualisation of intrinsic curvature

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Summary

We have undertaken molecular dynamics simulations on the d(CGCAAAAAAGCG)•d(CGCTTTTTTGCG) dodecamer in solution. In this study, we focus on aspects of conformation and dynamics, including the possibility of cross-strand hydrogen bonds. We compare our results with those from crystallography as well as infrared, Raman and NMR spectroscopy and cyclization kinetics. Our method of analysis allows us to visualise the curvature of the helix as a function of time during the simulation. We find that the major distortions of the helix axis path occur at the junctions between the (essentially straight) A-tract and the CG-and GC-tracts, although at one junction this is due to hyperflexibility (i.e., regions of high flexibility with no preferred direction of curvature), while at the other junction a static curvature is found (i.e., a preferred, sustained direction of curvature).

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Authors and Affiliations

  1. Department of Crystallography, Birkbeck College, Malet Street, WC1E 7HX, London, U.K.

    Osmar Norberto de Souza & Julia M. Goodfellow

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  1. Osmar Norberto de Souza
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  2. Julia M. Goodfellow
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de Souza, O.N., Goodfellow, J.M. Molecular dynamics simulations of oligonucleotides in solution: Visualisation of intrinsic curvature. J Computer-Aided Mol Des 8, 307–322 (1994). https://doi.org/10.1007/BF00126748

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  • DOI: https://doi.org/10.1007/BF00126748

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